TALE proteins of plant pathogenic bacteria in the genus Xanthomonas play important roles in disease, or trigger defense, by binding host DNA and activating effector-specific host genes (see, e.g., Gu et al., 2005, Nature 435:1122; Yang et al., 2006 Proc. Natl. Acad. Sci. USA 103:10503; Kay et al., 2007, Science 318:648; Sugio et al., 2007, Proc. Natl. Acad. Sci. USA 104:10720; and Romer et al., 2007, Science 318:645). Specificity for nucleic acid sequences depends on an effector-variable number of imperfect, typically ˜33-35 amino acid repeats (Schornack et al., 2006, J. Plant Physiol. 163:256). Each repeat binds to one nucleotide in the target sequence, and the specificity of each repeat for its nucleotide is largely context-independent, allowing for the development of custom sequence-specific TALE proteins (Moscou et al., 2009, Science 326:1501; Boch et al., 2009, Science 326:1509-1512).